Run ID: ERR2707123
Sample name:
Date: 19-10-2023 12:06:07
Number of reads: 2459728
Percentage reads mapped: 99.63
Strain: lineage4.6.1.2
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.99) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | R | pncA c.267_277delAATCGAGGCGG (0.98) |
| Streptomycin | ||
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.6 | Euro-American | T;LAM | None | 1.0 |
| lineage4.6.1 | Euro-American (Uganda) | T2 | RD724 | 1.0 |
| lineage4.6.1.2 | Euro-American | T2 | RD724 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2288964 | c.267_277delAATCGAGGCGG | frameshift_variant | 0.98 | pyrazinamide |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5078 | c.-162_-161insG | upstream_gene_variant | 0.97 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7539 | p.Thr80Ala | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| rpoC | 762926 | c.-444C>T | upstream_gene_variant | 1.0 |
| rpoC | 764810 | p.Pro481Thr | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| embR | 1416410 | p.Leu313Arg | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| ahpC | 2726121 | c.-72C>T | upstream_gene_variant | 0.99 |
| Rv2752c | 3065920 | p.Pro91Leu | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| rpoA | 3877960 | p.Val183Gly | missense_variant | 0.97 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243190 | c.-43G>C | upstream_gene_variant | 0.97 |
| embA | 4245055 | p.Thr608Asn | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407931 | p.Leu91Pro | missense_variant | 1.0 |
